I have a theory regrading Neo that seems to satisfy all contentious thoughts and threads on his persona and who he is. I've been reading the posts here and on the broader Net and find that most theories re: Neo are close but miss the most important point. i'm not going to delve into the philosophical religious contexts of the movies (cuz I don't know enough about them), but I think it's safe to say that everyone agrees that Neo is the Christian equivalent of Jesus Christ - came here to save (or FREE as Neo is falsely led to believe) humanity.
The most important parallel to draw here, however, is not what Neo (Christ) was sent to do, but who he is. Christ is the Son of God (God made incarnate taking human form). Neo is exactly the same - a program taking human form - the culmination of the machine's mastery over us: we first created machines which gave birth to A.I. They, in turn, 'grow' humans and embed them with programs.
The only distinction is that Jesus KNEW he was God come into human form. Neo, when first taken out of the Matrix in M1, is not yet 'self-aware' that he carries a code in his mind (recall the Arhcitect's conversation with Neo - "Although the prcoess has altered your mind, you remain irrevocable human...). The 'process' the Architect is referring to is the embedding of the program code within Neo which makes him the One. As we all now know, the One's purpose is to carry with him the experiences, interactions and choices he makes in his life so that when ultimately re-inserted into the CODE, make the next version of the Matrix consistently better and more realistic. Why do you think the machines become 'exceedingly effiecient at destroying Zion?' The ONE, therefore, is still human (like Jesus was), but also fully program, just not self-aware of his ultimate purpose.
This is exactly why Neo is able to do the things he is able to within the Matrix AND outside the Matrix (see code, move faster, quicker, etc). If the 'highest order machine' (for lack of a better term - and NOT the Architect) who thought of the concept of the Matrix did not embed this machine code within the One, the One would never have the ability to resist the Agents and eventually reach the CODE. It was the 'highest order machine's' intent to have the One to reach the CODE and reset the Matrix, thus continuing the never-ending cycle of control.
This is why Neo is able to come back to life in M1 (for which I've not seen a good explanation). Like Jesus, he is resurrected. But only after Trinity professes her love for him (as we are led to believe). We think the Oracle's foretelling of Trinity's fate (of falling in love with the One) brings Neo back from the grave, but in reality, it is his machine code that brings him back. Because Neo has machine code, the only way he can die within the Matrix is if he lets himself die or get deleted (as the Oracle said in M2, some programs face deletion and go away, others hide in the Matrix). At the point when we think he is dead, we can presume that his machine code's will to survive is still embedded in him b/c its purpose is as yet unfulfilled. As a result, the unfulfilled purpose of the code gives his human form enough strength to live again. It is at this point that Neo first becomes 'self aware' of his POWERS - as we see at the end of M1 and during M2, being fully machine yet fully human has it benefits.
During M2 he is not made aware of his PURPOSE until he finally meets the Architect. The Architect also states that 'his predecessors were, by design, based on a similar predication...' Although many posts discount this 'by design' phrase, I take it as the WB's very clever double entendre meant to have us think more confusing thoughts. I take its meaning as literal in the context of my "Neo is a human program" theory. The program embedded within Neo was designed by the 'highest order machine' to fulfill its purpose of re-inserting itself into the CODE and therefore meant to instill a sense of attachment to humanity in its host. thereby allowing the One to choose to reload the Matrix yet again, albeit via blackmail (i.e. if he didn't, every human would die). What the machines didn't count on, though, was that Neo would fall in love. Which is why he chooses to save Trinity, rather than have all humanity enslaved all over again. Neo choosing to fall in love was not part of his program - clearly any self preserving machine would not allow its host's decision to be confused and over-rided by love.
This also explains Neo's dreams and his conversation with the Oracle. Neo can see the future in his dreams because what he dreams occurs within the Matrix. Having this code within him provides this special ability. When he sees the Oracle, she asks him if he sees Trinity die. Neo states, "No..." He doesn't see her die because he saves her! - he just just doesn't know it yet. The Oracle DOES know however. She knows at that point that Neo, when faced with the choice of going into the CODE or saving Trinity, will choose to save Trinity because he loves her - a variable the machines did not account for. He, being thick headed, still doesn't understand it all. When they part, she says, "For what it's worth, you've made a believer out of me..." She, being the program created to investigate the human psyche (yes, I believe she is the Mother), could not fathom that the One faced with this choice would choose to save 1 person they had a profound attachment to rather than save all of humanity with whom no attachment existed. But love (which Neo is capable of b/c he is fully human) - the unknown variable - changed the rules. The is what she finally 'believes'. Neo was not predestined to save her as many speculate. He CHOOSES to save her b/c he loves her. It is his CHOICE.
As for Smith - he is the Matrix's Antichrist to Neo. A program within a program (The Matrix) that gains, like Neo does, self-awareness of his condition. Smith is nothing more than a program that went awry and grew A.I. He is able to traverse the Matrix and the real world because Neo imprinted himself into Smith at the end of M1. Neo, being both code and human, left remnant traces of himself when he destroyed Smith. Smith, as a result of his hatred for humanity and of his imprisonment within the Matrix (recall when he's talking to Morpheus in M1 about how he hates the constructed world - he calls it a 'zoo' and how he wants to be free of it), chooses exile within the Matrix rather than face deletion and moreover, now has the ability to go into the real world. He is, in essence, the ironic product of free will that gave rise to the machines' revolt against the humans when they (humans) first spawned robots (a la Animatrix Episodes), except that he was created by machines as well. Now by being able to replicate himself, he threatens the very system by which both humans and machines live: the symbiotic Matrix. As much as the humans and machines hate to admit it, they both need one another. Smith, being a virus, threatens that very balance. Revolutions will answer the question.
Okay, I went a little farther than I intended. Feel free to comment. I'm interested in hearing your thoughts.